@figtreejs/core 0.1.0-beta.3 → 0.1.0-beta.4

package/dist/index.cjs

@@ -1,2 +1,2 @@
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g=Mr(t.to),{config:m}=o,{decay:x,velocity:p}=m;(r||i)&&(m.velocity=0),t.config&&!g&&tu(m,He(t.config,a),t.config!==s.config?He(s.config,a):void 0);let b=Se(this);if(!b||_.und(c))return n(ve(this,!0));const y=_.und(t.reset)?i&&!t.default:!_.und(h)&&Lt(t.reset,a),w=y?h:this.get(),C=Vt(c),k=_.num(C)||_.arr(C)||Bn(C),A=!g&&(!k||Lt(s.immediate||t.immediate,a));if(d){const N=Cr(c);if(N!==b.constructor)if(A)b=this._set(C);else throw Error(`Cannot animate between ${b.constructor.name} and ${N.name}, as the "to" prop suggests`)}const E=b.constructor;let I=de(c),j=!1;if(!I){const N=y||!tr(this)&&f;(d||N)&&(j=Ee(Vt(w),C),I=!j),(!Ee(o.immediate,A)&&!A||!Ee(m.decay,x)||!Ee(m.velocity,p))&&(I=!0)}if(j&&Le(this)&&(o.changed&&!y?I=!0:I||this._stop(l)),!g&&((I||de(l))&&(o.values=b.getPayload(),o.toValues=de(c)?null:E==Nn?[1]:he(C)),o.immediate!=A&&(o.immediate=A,!A&&!y&&this._set(l)),I)){const{onRest:N}=o;O(au,M=>Bi(this,t,M));const L=ve(this,St(this,l));Rt(this._pendingCalls,L),this._pendingCalls.add(n),o.changed&&R.batchedUpdates(()=>{o.changed=!y,N?.(L,this),y?He(s.onRest,L):o.onStart?.(L,this)})}y&&this._set(w),g?n(is(t.to,t,this._state,this)):I?this._start():Le(this)&&!d?this._pendingCalls.add(n):n(rs(w))}_focus(e){const t=this.animation;e!==t.to&&(Pi(this)&&this._detach(),t.to=e,Pi(this)&&this._attach())}_attach(){let e=0;const{to:t}=this.animation;de(t)&&(xt(t,this),$r(t)&&(e=t.priority+1)),this.priority=e}_detach(){const{to:e}=this.animation;de(e)&&zt(e,this)}_set(e,t=!0){const n=ae(e);if(!_.und(n)){const r=Se(this);if(!r||!Ee(n,r.getValue())){const i=Cr(n);!r||r.constructor!=i?ii(this,i.create(n)):r.setValue(n),r&&R.batchedUpdates(()=>{this._onChange(n,t)})}}return Se(this)}_onStart(){const e=this.animation;e.changed||(e.changed=!0,$t(this,"onStart",ve(this,St(this,e.to)),this))}_onChange(e,t){t||(this._onStart(),He(this.animation.onChange,e,this)),He(this.defaultProps.onChange,e,this),super._onChange(e,t)}_start(){const e=this.animation;Se(this).reset(ae(e.to)),e.immediate||(e.fromValues=e.values.map(t=>t.lastPosition)),Le(this)||(Oi(this,!0),Mt(this)||this._resume())}_resume(){Ne.skipAnimation?this.finish():On.start(this)}_stop(e,t){if(Le(this)){Oi(this,!1);const n=this.animation;O(n.values,i=>{i.done=!0}),n.toValues&&(n.onChange=n.onPause=n.onResume=void 0),jt(this,{type:"idle",parent:this});const r=t?ot(this.get()):ve(this.get(),St(this,e??n.to));Rt(this._pendingCalls,r),n.changed&&(n.changed=!1,$t(this,"onRest",r,this))}}};function St(e,t){const n=Vt(t),r=Vt(e.get());return Ee(r,n)}function os(e,t=e.loop,n=e.to){const r=He(t);if(r){const i=r!==!0&&ts(r),a=(i||e).reverse,s=!i||i.reset;return Ht({...e,loop:t,default:!1,pause:void 0,to:!a||Mr(n)?n:void 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Names must be unique`);n=lc(r,this._data.allNames.length)}else{if(n=t,Object.prototype.hasOwnProperty.call(this._data.byName,n.name))throw new Error(`taxon ${n.name} already exists in the set. Names must be unique`);if(this._data.allNames[n.number]&&this._data.allNames[n.number]!==n.name)throw new Error(`taxon number ${n.number} already exists in the set with name ${this._data.allNames[n.number]}. 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A node must be provided if the first value is not an array");const r=[...this.getPathToRoot(t)];let i=null;for(const a of this.getPathToRoot(n))if(r.includes(a)){i=a;break}if(i===null)throw new Error("No MRCA found");return i}}getPath(t,n){const r=[],i=this.getMRCA(t,n);for(let a of[t,n])for(;a!=i;)r.push(a),a=this.getParent(a);return r}getPathLength(t,n){let r=0;const i=this.getMRCA(t,n);for(let a of[t,n])for(;a!=i;){const s=this.getLength(a);r+=s,a=this.getParent(a)}return r}*getPathToRoot(t){let n=t;for(;!this.isRoot(n);)yield n,n=this.getParent(n);yield n}getNextSibling(t){if(!this.hasLeftSibling(t)&&!this.hasRightSibling(t))throw new Error(`Node ${t.number} has no sibling`);const n=this.getParent(t),r=n.children.map(i=>i).indexOf(t.number);return this.getChild(n,(r+1)%this.getChildCount(n))}hasRightSibling(t){const n=fr(this,t);switch(n.type){case V.Nothing:return!1;case V.Some:return n.value.children.map(r=>r).indexOf(t.number)<this.getChildCount(n.value)-1}}getRightSibling(t){if(!this.hasRightSibling(t))throw new Error(`node ${t.number} does not have a right sibling`);const n=this.getParent(t),r=n.children.map(i=>i).indexOf(t.number);return this.getChild(n,r+1)}hasLeftSibling(t){const n=fr(this,t);switch(n.type){case V.Nothing:return!1;case V.Some:return this.getChildCount(n.value)>1&&n.value.children.map(r=>r).indexOf(t.number)>0}}getLeftSibling(t){if(!this.hasLeftSibling(t))throw new Error(`node ${t.number} does not have a left sibling`);const n=this.getParent(t),r=n.children.map(i=>i).indexOf(t.number);return this.getChild(n,r-1)}getDivergence(t){let n=0;for(const r of this.getPathToRoot(t))this.isRoot(r)?this.hasBranchLength(r)&&(n+=this.getLength(r)):n+=this.getLength(r);return n}getChildCount(t){if(!this._data.nodes.allNodes[t.number])throw new Error(`Node ${t.number} not found`);return this._data.nodes.allNodes[t.number].children.length}getChild(t,n){return this._data.nodes.allNodes[this._data.nodes.allNodes[t.number].children[n]]}getParent(t){const n=fr(this,t);switch(n.type){case V.Some:return n.value;case V.Nothing:throw new Error(`No parent for node ${t.number}`)}}getChildren(t){return this._data.nodes.allNodes[t.number].children.map(n=>this.getNode(n))}hasLabel(t){return this._data.nodes.allNodes[t.number].label!==void 0}getLabel(t){const n=this._data.nodes.allNodes[t.number].label;if(n===void 0)throw new Error(`no label for node ${t.number}`);return n}isExternal(t){return this.getNode(t.number).children.length===0}isInternal(t){return this.getNode(t.number).children.length>0}isRoot(t){return this._data.rootNode===t.number}addNodes(t=1){const n=[];return{tree:J(this,r=>{const i=r._data.nodes.allNodes.length;for(let a=0;a<t;a++){const s={number:i+a,children:[],parent:void 0,label:void 0,length:void 0,taxon:void 0,annotations:{},_id:hn()};n.push(s),r._data.nodes.allNodes.push(s)}}),nodes:n}}setTaxon(t,n){if(n!==this.taxonSet.getTaxonByName(n.name))throw new Error(`Taxon ${n.name} is either not in the taxon set. Has it been copied?`);return J(this,r=>{const i=r.getNode(t.number);i.taxon=n.number,r._data.nodes.byTaxon[n.number]=t.number,r._data.nodeToTaxon[t.number]=n.number})}getAnnotationSummary(t){if(this._data.annotations[t]===void 0)throw new Error(`No annotation with name ${t} found in tree`);return this._data.annotations[t]}getAnnotations(){return Object.values(this._data.annotations)}getAnnotation(t,n,r){const i=hr(this,this.getNode(t.number),n);if(r===void 0){const{value:a}=Gi(i,`Node ${t.number} is not annotated with ${n}`);return a}else switch(i.type){case V.Some:return i.value.value;case V.Nothing:return r}}getFullNodeAnnotation(t,n){const r=hr(this,this.getNode(t.number),n);return Gi(r,`Node ${t.number} is not annotated with ${n}`)}hasAnnotation(t,n){switch(hr(this,this.getNode(t.number),n).type){case V.Some:return!0;case V.Nothing:return!1}}annotateNode(t,n,r){if(typeof n=="string"){const i=n,s=Yu(r),o=this._data.annotations[i];if(o!==void 0&&o.type!==s.type)throw new Error(`Tried annotation ${i} was parsed as ${s.type} - but is ${o.type} in tree.`);return J(this,l=>{const u=o?o.domain:void 0,c=Bc(s,u);l._data.nodes.allNodes[t.number].annotations[i]={id:i,type:s.type,value:s.value},l._data.annotations[i]={id:i,type:s.type,domain:c}})}else{let i=this;for(const[a,s]of Object.entries(n))i=i.annotateNode(t,a,s);return i}}setHeight(t,n){if(!this.hasLengths())throw new Error("Can not set the heights of nodes in a tree without branch lengths");return J(this,r=>{const i=r.getNode(t.number);if(n<0)throw new Error("Height must be non-negative");const s=r.getHeight(t)-n;if(i.length===void 0){if(!r.isRoot(t))throw new Error("Cannot set height on a node without length")}else i.length=i.length+s;for(const o of r.getChildren(t)){const l=r.getNode(o.number),u=r.getLength(l)-s;l.length=u}})}setLength(t,n){return J(this,r=>{const i=r.getNode(t.number);i.length=n,r._data.hasLengths=!0})}deleteLength(t){return J(this,n=>{const r=n.getNode(t.number);r.length=void 0})}setDivergence(t,n){if(!this.hasLengths())throw new Error("Can not set the divergences of nodes in a tree without branch lengths");return J(this,r=>{const i=r.getNode(t.number),a=r.getHeight(t),l=r.getHeight(r.getRoot())-a-n,u=r.getLength(t);i.length=u-l})}setLabel(t,n){if(this._data.nodes.byLabel[n]!==void 0)throw new Error(`Duplicate node label ${n}`);return J(this,r=>{const i=r.getNode(t.number);i.label=n,r._data.nodes.byLabel[n]=t.number})}insertNode(t,n=.5){return J(this,r=>{const i={number:r._data.nodes.allNodes.length,children:[],parent:void 0,label:"",length:void 0,taxon:void 0,annotations:{},_id:hn()};r._data.nodes.allNodes.push(i),r._data.nodes.byTaxon.length+=1;const a=r.getNode(t.number),s=r.getParent(a),o=s.children.indexOf(a.number);s.children.splice(o,1,i.number),i.parent=s.number;const u=r.getLength(a);a.length=u*(1-n),i.length=u*n,i.children=[a.number],a.parent=i.number})}unroot(t){throw new Error("unroot not implemented in immutable tree")}deleteNode(t){throw new Error("deleteNode not implemented in immutable tree")}deleteClade(t){throw new Error("deleteClade not implemented in immutable tree")}orderNodesByDensity(t,n){return J(this,r=>{n===void 0&&(n=r._data.nodes.allNodes[r._data.rootNode]);const i=t?1:-1;Us(r._data,n,(a,s,o,l)=>(s-l)*i)})}rotate(t,n=!1){return J(this,r=>{const i=r.getNode(t.number);if(i.children=i.children.reverse(),n)for(const a of i.children.map(s=>r.getNode(s)))r.rotate(a,n)})}reroot(t,n=.5){return J(this,r=>{if(t.number===r._data.rootNode)return;const i=r.getRoot();i.children.length!==2&&console.warn("Root node has more than two children and we are rerooting! There be dragons!");let a=0;if(i.children.length==2)a=i.children.map(o=>r.getNode(o)).map(o=>r.getLength(o)).reduce((o,l)=>l+o,0);else{const o=[...r.getPathToRoot(t)],l=o[o.length-2];if(K(l,"Index error when looking for the root child"),!i.children.includes(l.number))throw new Error("Root child not in path to root - likely an internal error");a=r.getLength(l)}const s=r.getNode(t.number);if(r.getParent(t)!==i){let o=s,l=r.getParent(s);const u=r.getChild(l,0).number===t.number,c=s,h=l;let f=r.getLength(l);for(;!r.isRoot(l);){if(l.children=l.children.filter(g=>g!==o.number),r.getParent(l).number===i.number)if(i.children.length==2){if(!r.hasLeftSibling(l)&&!r.hasRightSibling(l))throw new Error("no sibling in rerooting");const m=r.hasLeftSibling(l)?r.getLeftSibling(l):r.getRightSibling(l);l.children.push(m.number),m.parent=l.number,m.length=a}else{const g={number:r._data.nodes.allNodes.length,children:[],parent:void 0,label:"",length:void 0,taxon:void 0,annotations:{},_id:hn()};r._data.nodes.allNodes.push(g),g.length=a,l.children.push(g.number),g.parent=l.number;for(const m of i.children){const x=r.getNode(m);x.number!==l.number&&(x.parent=g.number,g.children.push(x.number))}}else{const g=r.getParent(l),m=r.getLength(g);g.length=f,f=m,l.children.push(g.number)}o=l,l=r.getParent(l)}c.parent=i.number,h.parent=i.number,i.children=[c.number,h.number],u||(i.children=i.children.reverse()),this.getInternalNodes().forEach(g=>{for(const m of r.getChildren(g))m.parent=g.number});const d=r.getLength(c)*n;h.length=d,K(c.length,"Expected the root's new child to have a length"),c.length-=d}else{const o=r.getLength(t)*(1-n);s.length=o;const l=r.getNextSibling(t);l.length=a-o}})}removeChild(t,n){return J(this,r=>{r._data.nodes.allNodes[t.number].children=r._data.nodes.allNodes[t.number].children.filter(i=>i!==n.number),r._data.nodes.allNodes[n.number].parent=-1})}sortChildren(t,n){return J(this,r=>{r._data.nodes.allNodes[t.number].children=this._data.nodes.allNodes[t.number].children.map(i=>r.getNode(i)).sort(n).map(i=>i.number)})}addChild(t,n){return J(this,r=>{const i=r.getNode(n.number);r.getNode(t.number).children.push(i.number),i.parent=t.number})}setRoot(t){return J(this,n=>{n._data.rootNode=t.number})}}function Us(e,t,n){let r=0;if(e.nodes.allNodes[t.number].children.length>0){const i=new Map;for(const o of e.nodes.allNodes[t.number].children.map(l=>e.nodes.allNodes[l])){const l=Us(e,o,n);i.set(o.number,l),r+=l}const a=e.nodes.allNodes[t.number].children.slice().sort((o,l)=>n(e.nodes.allNodes[o],ye(i.get(o),"Internal error when ordering. Counts not defined."),e.nodes.allNodes[l],ye(i.get(l),"Internal error when ordering. Counts not defined.")));a.reduce((o,l,u)=>o||l!==e.nodes.allNodes[t.number].children[u],!0)&&(e.nodes.allNodes[t.number].children=a)}else r=1;return r}function*Oc(e,t=void 0){const n=function*(r){yield e.getNode(r.number);const i=e.getChildCount(r);if(i>0)for(let a=0;a<i;a++){const s=e.getChild(r,a);yield*n(s)}};t===void 0&&(t=e.getRoot()),yield*n(t)}function*jc(e,t=void 0){const n=function*(r,i=void 0){const a=[...e.getChildren(r)];e.isRoot(r)||a.push(e.getParent(r));const s=a.filter(u=>u.number!==i),o=a.find(u=>u.number===i);let l;!e.isRoot(r)&&o===e.getParent(r)?l=e.getLength(r):o!==void 0&&(l=e.getLength(o));for(const u of s)yield*n(u,r.number);yield{...e.getNode(r.number),pseudoLength:l,pseudoChildren:s,pseudoParent:o}};t===void 0&&(t=e.getRoot()),yield*n(t)}function*Os(e,t=void 0){const n=function*(r,i=void 0){const a=[...e.getChildren(r)];e.isRoot(r)||a.push(e.getParent(r));const s=a.filter(u=>u.number!==i),o=a.find(u=>u.number===i);let l;!e.isRoot(r)&&o===e.getParent(r)?l=e.getLength(r):o!==void 0&&(l=e.getLength(o)),yield{...e.getNode(r.number),pseudoLength:l,pseudoChildren:s,pseudoParent:o};for(const u of s)yield*n(u,r.number)};t===void 0&&(t=e.getRoot()),yield*n(t)}function*js(e,t,n){const r=function*(i,a=void 0){const s=[...e.getChildren(i)];e.isRoot(i)||s.push(e.getParent(i));const o=s.filter(c=>c.number!==a),l=s.find(c=>c.number===a);let u;if(!e.isRoot(i)&&l===e.getParent(i)?u=e.getLength(i):l!==void 0&&(u=e.getLength(l)),o.length==0)yield{...e.getNode(i.number),pseudoLength:u,pseudoChildren:o,pseudoParent:l};else for(const c of o)yield*r(c,i.number)};t===void 0&&(t=e.getRoot()),n!==void 0?yield*r(t,n.number):yield*r(t)}function*zs(e,t=void 0){const n=function*(r){const i=e.getChildCount(r);if(i>0)for(let a=0;a<i;a++){const s=e.getChild(r,a);yield*n(s)}yield r};t===void 0&&(t=e.getRoot()),yield*n(t)}function*bi(e,t){t===void 0&&(t=e.getRoot());const n=function*(r){const i=e.getChildCount(r);if(i>0)for(let a=0;a<i;a++){const s=e.getChild(r,a);yield*n(s)}else yield r};yield*n(t)}function*zc(e,t){let n=t;for(;!e.isRoot(n);)yield n,n=e.getParent(n);yield n}function Bc(e,t){switch(e.type){case q.BOOLEAN:return[!0,!1];case q.DISCRETE:{const n=e.value;if(t!==void 0){const r=t;return[...new Set([...r,n])].sort()}else return[n]}case q.NUMERICAL:{const n=e.value;return ct([...t||[],n])}case q.DISCRETE_SET:{const n=e.value,r=t||[];return[...new Set([...r,...n])].sort()}case q.NUMERICAL_SET:{const n=e.value;return ct([...t||[],...n])}case q.DENSITIES:if(t!==void 0){const n=t;return[...new Set([...n,...Object.keys(e.value)])].sort()}else return[...new Set(Object.keys(e.value))].sort().filter(n=>n);case q.MARKOV_JUMPS:{const n=e.value.reduce((i,a)=>i.concat([a.to,a.from]),[]),r=t||[];return[...new Set([...r,...n])].sort()}default:throw new Error("Unrecognized type  when updating domain")}}function Vc(){return{lastChunk:"",status:"parsing",end:"",start(){},transform(e,t){const n=this.lastChunk+e;let r="";for(let i=0;i<n.length;i++){const a=n[i];K(a,"Internal Error. Hit empty character in array"),this.status==="parsing"?([this.status,this.end]=qc(a),this.status==="in comment"&&(r.length>0&&t.enqueue(r),r="")):a===this.end&&(this.status="parsing",this.end=""),this.status==="parsing"&&/\s|;|\]/.test(a)?(r.length>0&&(/\]/.test(a)&&(r+=a),t.enqueue(r),r=""),/;/.test(a)&&t.enqueue(a)):r+=a}this.lastChunk=r},flush(e){this.lastChunk&&e.enqueue(this.lastChunk)}}}function qc(e){return e==="'"?["in single quote","'"]:e==='"'?["in double quote",'"']:e==="["?["in comment","]"]:["parsing",""]}const ma=/\s*('[^']+'|"[^"]+"|\[&[^[]+]|,|:|\)|\(|;)\s*/;class Hc{reader;taxonSet;currentBlock;hasTree;options;translateTaxonMap;constructor(t,n={}){const r=new TransformStream(Vc());this.reader=t.pipeThrough(new TextDecoderStream).pipeThrough(r).getReader(),this.taxonSet=new rn,this.currentBlock=void 0,this.options=n}async*getTrees(){for(;this.currentBlock!=="trees";)await this.parseNextBlock(),this.hasTree=!0;yield*this.parseTreesBlock()}async parseNextBlock(){const t=await this.getNextBlockName();switch(t){case"taxa":this.currentBlock="taxa",await this.parseTaxaBlock();break;case"trees":this.currentBlock="trees";break;default:console.log(`skipping block ${t}. Only parsing blocks are taxa and trees for now.`),await this.readToEndOfBlock()}}async nextToken(){const{done:t,value:n}=await this.reader.read();if(t)throw new Error("unexpectedly hit the end of the stream");return n}async skipSemiColon(){const{done:t,value:n}=await this.reader.read();if(t)throw new Error("unexpectedly hit the end of the stream");if(!n.match(/;$/))throw new Error(`expected ";" got ${n}`)}async getNextBlockName(){let t=!0,n;for(;t;)(await this.nextToken()).match(/\bbegin/i)&&(n=await this.nextToken(),await this.skipSemiColon(),t=!1);return n}async readToEndOfBlock(){let t=!0;for(;t;)(await this.nextToken()).match(/\bend;/i)&&(t=!1)}async skipUntil(t){let n,r=!0;for(;r;)n=await this.nextToken(),t.test(n)&&(r=!1);if(n==null)throw new Error(`Internal parsing error: ${t.source} not found `);return n}async readUntil(t){let n="",r=!0;for(;r;){const i=await this.nextToken();t.test(i)&&(n+=i,r=!1),n+=i}return n}async parseTaxaBlock(){let t,n=!0;for(;n;){const r=await this.skipUntil(/dimensions|taxlabels|end/i);switch(!0){case/dimensions/i.test(r):{const i=await this.readUntil(/;/),a=i.match(/ntax=(\d+);/);if(a)K(a[1],"No number of taxa found despite matching regex"),t=parseInt(a[1]);else throw new Error(`Expected dimension in form of ntax=(\\d+);. Got ${i}`);break}case/taxlabels/i.test(r):{let i=await this.nextToken();for(;i!==";";)this.taxonSet.addTaxon(i),i=await this.nextToken();if(t&&t!=this.taxonSet.getTaxonCount())throw new Error(`found ${this.taxonSet.getTaxonCount()} taxa. Expected: ${t}}`);break}case/end/i.test(r):{if(this.taxonSet.getTaxonCount()===0)throw new Error("hit end of taxa section but didn't find any taxa");this.taxonSet.lockTaxa(),await this.skipSemiColon(),n=!1;break}default:throw new Error(`Reached impossible code looking for dimensions or taxlabels or end in taxa block "${r}"`)}}}async*parseTreesBlock(){let t,n=!0;for(;n;){const r=await this.skipUntil(/translate|tree|end/i);switch(!0){case/translate/i.test(r):{this.translateTaxonMap=new Map;let i=0,a;for(t=await this.nextToken();t!==";";){if(i%2==0)a=t;else{if(t[t.length-1]===","&&(t=t.slice(0,-1)),this.taxonSet.isFinalized){if(!this.taxonSet.hasTaxon(t))throw new Error(`Taxon ${t} not found in taxa block - but found in translate block`)}else this.taxonSet.addTaxon(t);K(a,"Error parsing nexus. Expected key for taxa but found nothing"),this.translateTaxonMap.set(a,t)}for(t=await this.nextToken();t===",";)t=await this.nextToken();i++}this.taxonSet.lockTaxa();break}case/tree/i.test(r):{await this.nextToken();const i=new $s(this.taxonSet,{translateTaxonNames:this.translateTaxonMap});t=await this.skipUntil(/\(/);let a=t.split(ma).filter(o=>o.length>0).reverse();for(;!i.isDone();){for(;a.length>0;){const o=a.pop();K(o,"Unexpectedly hit the end of the buffer"),i.parseCharacter(o)}i.isDone()||(t=await this.nextToken(),a=t.split(ma).filter(o=>o.length>0).reverse())}yield i.getTree();break}case/end/i.test(r):await this.skipSemiColon(),this.hasTree=!1,this.reader.releaseLock(),n=!1;break;default:throw new Error(`Reached impossible code in treeblock block "${r}"`)}}}}class Yc{_forwardCache;_reverseCache;constructor(){this._forwardCache=new Map,this._reverseCache=new Map}*traverse(t,n){const r=function*(i){const a=t.getChildCount(i);if(a>0)for(let s=0;s<a;s++){const o=t.getChild(i,s);yield*r(o)}yield i};n===void 0&&(n=t.getRoot()),yield*r(n)}getNext(t,n){const r=this._forwardCache.get(n);if(r!==void 0&&this._forwardCache.get(r)!==void 0)return r;if(t.isRoot(n))return;const i=t.getParent(n);if(t.hasRightSibling(n)){const a=t.getRightSibling(n);this._forwardCache.set(n,a),this._reverseCache.set(a,n)}else this._forwardCache.set(n,i),this._reverseCache.set(i,n);return this._forwardCache.get(n)}getPrevious(t,n){const r=this._reverseCache.get(n);if(r!==void 0&&this._reverseCache.get(r)!==void 0)return r;if(n!==this.traverse(t).next().value){if(t.isInternal(n)){const i=t.getChildCount(n)-1,a=t.getChild(n,i);this._reverseCache.set(n,a),this._forwardCache.set(a,n)}else if(t.hasLeftSibling(n)){const i=t.getLeftSibling(n);this._reverseCache.set(n,i),this._forwardCache.set(i,n)}else{let i=n;for(;!t.hasLeftSibling(i);)i=t.getParent(i);const a=t.getLeftSibling(i);this._reverseCache.set(n,a),this._forwardCache.set(a,n)}return this._reverseCache.get(n)}}}var 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n-this.getDivergence(t)}hasBranchLength(t){return this.getNode(t.number).length!==void 0}getLength(t){const r=this.getNode(t.number).length;if(r===void 0){if(this.hasLengths())throw new Error(`The tree has lengths but, no length was found for node ${t.number}`);return console.warn("The tree does not have branchlengths so a length of 1 is used as default"),1}return r}hasLengths(){return this._data.hasLengths}_toString(t,n){return n===void 0&&(n={blFormat:Zt("0.2"),includeAnnotations:!1}),(this.getChildCount(t)>0?`(${this.getChildren(t).map(r=>this._toString(r,n)).join(",")})${this.hasLabel(t)?"#"+this.getLabel(t):""}`:this.hasTaxon(t)?this.getTaxonFromNode(t).name:"")+(n.includeAnnotations?this._writeAnnotations(t):"")+(this.hasBranchLength(t)?`:${n.blFormat(this.getLength(t))}`:"")}_writeAnnotations(t){const n=this._data.nodes.allNodes[t.number].annotations;if(Object.keys(n).length===0)return"";let r="[&",i=0;for(const[a,s]of Object.entries(n))i>0&&(r+=", 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A node must be provided if the first value is not an array");const r=[...this.getPathToRoot(t)];let i=null;for(const a of this.getPathToRoot(n))if(r.includes(a)){i=a;break}if(i===null)throw new Error("No MRCA found");return i}}getPath(t,n){const r=[],i=this.getMRCA(t,n);for(let a of[t,n])for(;a!=i;)r.push(a),a=this.getParent(a);return r}getPathLength(t,n){let r=0;const i=this.getMRCA(t,n);for(let a of[t,n])for(;a!=i;){const s=this.getLength(a);r+=s,a=this.getParent(a)}return r}*getPathToRoot(t){let n=t;for(;!this.isRoot(n);)yield n,n=this.getParent(n);yield n}getNextSibling(t){if(!this.hasLeftSibling(t)&&!this.hasRightSibling(t))throw new Error(`Node ${t.number} has no sibling`);const n=this.getParent(t),r=n.children.map(i=>i).indexOf(t.number);return this.getChild(n,(r+1)%this.getChildCount(n))}hasRightSibling(t){const n=dr(this,t);switch(n.type){case V.Nothing:return!1;case V.Some:return n.value.children.map(r=>r).indexOf(t.number)<this.getChildCount(n.value)-1}}getRightSibling(t){if(!this.hasRightSibling(t))throw new Error(`node ${t.number} does not have a right sibling`);const n=this.getParent(t),r=n.children.map(i=>i).indexOf(t.number);return this.getChild(n,r+1)}hasLeftSibling(t){const n=dr(this,t);switch(n.type){case V.Nothing:return!1;case V.Some:return this.getChildCount(n.value)>1&&n.value.children.map(r=>r).indexOf(t.number)>0}}getLeftSibling(t){if(!this.hasLeftSibling(t))throw new Error(`node ${t.number} does not have a left sibling`);const n=this.getParent(t),r=n.children.map(i=>i).indexOf(t.number);return this.getChild(n,r-1)}getDivergence(t){let n=0;for(const r of this.getPathToRoot(t))this.isRoot(r)?this.hasBranchLength(r)&&(n+=this.getLength(r)):n+=this.getLength(r);return n}getChildCount(t){if(!this._data.nodes.allNodes[t.number])throw new Error(`Node ${t.number} not found`);return this._data.nodes.allNodes[t.number].children.length}getChild(t,n){return this._data.nodes.allNodes[this._data.nodes.allNodes[t.number].children[n]]}getParent(t){const n=dr(this,t);switch(n.type){case V.Some:return n.value;case V.Nothing:throw new Error(`No parent for node ${t.number}`)}}getChildren(t){return this._data.nodes.allNodes[t.number].children.map(n=>this.getNode(n))}hasLabel(t){return this._data.nodes.allNodes[t.number].label!==void 0}getLabel(t){const n=this._data.nodes.allNodes[t.number].label;if(n===void 0)throw new Error(`no label for node ${t.number}`);return n}isExternal(t){return this.getNode(t.number).children.length===0}isInternal(t){return this.getNode(t.number).children.length>0}isRoot(t){return this._data.rootNode===t.number}addNodes(t=1){const n=[];return{tree:J(this,r=>{const i=r._data.nodes.allNodes.length;for(let a=0;a<t;a++){const s={number:i+a,children:[],parent:void 0,label:void 0,length:void 0,taxon:void 0,annotations:{},_id:fn()};n.push(s),r._data.nodes.allNodes.push(s)}}),nodes:n}}setTaxon(t,n){if(n!==this.taxonSet.getTaxonByName(n.name))throw new Error(`Taxon ${n.name} is either not in the taxon set. Has it been copied?`);return J(this,r=>{const i=r.getNode(t.number);i.taxon=n.number,r._data.nodes.byTaxon[n.number]=t.number,r._data.nodeToTaxon[t.number]=n.number})}getAnnotationSummary(t){if(this._data.annotations[t]===void 0)throw new Error(`No annotation with name ${t} found in tree`);return this._data.annotations[t]}getAnnotations(){return Object.values(this._data.annotations)}getAnnotation(t,n,r){const i=fr(this,this.getNode(t.number),n);if(r===void 0){const{value:a}=Qi(i,`Node ${t.number} is not annotated with ${n}`);return a}else switch(i.type){case V.Some:return i.value.value;case V.Nothing:return r}}getFullNodeAnnotation(t,n){const r=fr(this,this.getNode(t.number),n);return Qi(r,`Node ${t.number} is not annotated with ${n}`)}hasAnnotation(t,n){switch(fr(this,this.getNode(t.number),n).type){case V.Some:return!0;case V.Nothing:return!1}}annotateNode(t,n,r){if(typeof n=="string"){const i=n,s=Gu(r),o=this._data.annotations[i];if(o!==void 0&&o.type!==s.type)throw new Error(`Tried annotation ${i} was parsed as ${s.type} - but is ${o.type} in tree.`);return J(this,l=>{const u=o?o.domain:void 0,c=qc(s,u);l._data.nodes.allNodes[t.number].annotations[i]={id:i,type:s.type,value:s.value},l._data.annotations[i]={id:i,type:s.type,domain:c}})}else{let i=this;for(const[a,s]of Object.entries(n))i=i.annotateNode(t,a,s);return i}}setHeight(t,n){if(!this.hasLengths())throw new Error("Can not set the heights of nodes in a tree without branch lengths");return J(this,r=>{const i=r.getNode(t.number);if(n<0)throw new Error("Height must be non-negative");const s=r.getHeight(t)-n;if(i.length===void 0){if(!r.isRoot(t))throw new Error("Cannot set height on a node without length")}else i.length=i.length+s;for(const o of r.getChildren(t)){const l=r.getNode(o.number),u=r.getLength(l)-s;l.length=u}})}setLength(t,n){return J(this,r=>{const i=r.getNode(t.number);i.length=n,r._data.hasLengths=!0})}deleteLength(t){return J(this,n=>{const r=n.getNode(t.number);r.length=void 0})}setDivergence(t,n){if(!this.hasLengths())throw new Error("Can not set the divergences of nodes in a tree without branch lengths");return J(this,r=>{const i=r.getNode(t.number),a=r.getHeight(t),l=r.getHeight(r.getRoot())-a-n,u=r.getLength(t);i.length=u-l})}setLabel(t,n){if(this._data.nodes.byLabel[n]!==void 0)throw new Error(`Duplicate node label ${n}`);return J(this,r=>{const i=r.getNode(t.number);i.label=n,r._data.nodes.byLabel[n]=t.number})}insertNode(t,n=.5){return J(this,r=>{const i={number:r._data.nodes.allNodes.length,children:[],parent:void 0,label:"",length:void 0,taxon:void 0,annotations:{},_id:fn()};r._data.nodes.allNodes.push(i),r._data.nodes.byTaxon.length+=1;const a=r.getNode(t.number),s=r.getParent(a),o=s.children.indexOf(a.number);s.children.splice(o,1,i.number),i.parent=s.number;const u=r.getLength(a);a.length=u*(1-n),i.length=u*n,i.children=[a.number],a.parent=i.number})}unroot(t){throw new Error("unroot not implemented in immutable tree")}deleteNode(t){throw new Error("deleteNode not implemented in immutable tree")}deleteClade(t){throw new Error("deleteClade not implemented in immutable tree")}orderNodesByDensity(t,n){return J(this,r=>{n===void 0&&(n=r._data.nodes.allNodes[r._data.rootNode]);const i=t?1:-1;Os(r._data,n,(a,s,o,l)=>(s-l)*i)})}rotate(t,n=!1){return J(this,r=>{const i=r.getNode(t.number);if(i.children=i.children.reverse(),n)for(const a of i.children.map(s=>r.getNode(s)))r.rotate(a,n)})}reroot(t,n=.5){return J(this,r=>{if(t.number===r._data.rootNode)return;const i=r.getRoot();i.children.length!==2&&console.warn("Root node has more than two children and we are rerooting! There be dragons!");let a=0;if(i.children.length==2)a=i.children.map(o=>r.getNode(o)).map(o=>r.getLength(o)).reduce((o,l)=>l+o,0);else{const o=[...r.getPathToRoot(t)],l=o[o.length-2];if(K(l,"Index error when looking for the root child"),!i.children.includes(l.number))throw new Error("Root child not in path to root - likely an internal error");a=r.getLength(l)}const s=r.getNode(t.number);if(r.getParent(t)!==i){let o=s,l=r.getParent(s);const u=r.getChild(l,0).number===t.number,c=s,h=l;let f=r.getLength(l);for(;!r.isRoot(l);){if(l.children=l.children.filter(g=>g!==o.number),r.getParent(l).number===i.number)if(i.children.length==2){if(!r.hasLeftSibling(l)&&!r.hasRightSibling(l))throw new Error("no sibling in rerooting");const m=r.hasLeftSibling(l)?r.getLeftSibling(l):r.getRightSibling(l);l.children.push(m.number),m.parent=l.number,m.length=a}else{const g={number:r._data.nodes.allNodes.length,children:[],parent:void 0,label:"",length:void 0,taxon:void 0,annotations:{},_id:fn()};r._data.nodes.allNodes.push(g),g.length=a,l.children.push(g.number),g.parent=l.number;for(const m of i.children){const x=r.getNode(m);x.number!==l.number&&(x.parent=g.number,g.children.push(x.number))}}else{const g=r.getParent(l),m=r.getLength(g);g.length=f,f=m,l.children.push(g.number)}o=l,l=r.getParent(l)}c.parent=i.number,h.parent=i.number,i.children=[c.number,h.number],u||(i.children=i.children.reverse()),this.getInternalNodes().forEach(g=>{for(const m of r.getChildren(g))m.parent=g.number});const d=r.getLength(c)*n;h.length=d,K(c.length,"Expected the root's new child to have a length"),c.length-=d}else{const o=r.getLength(t)*(1-n);s.length=o;const l=r.getNextSibling(t);l.length=a-o}})}removeChild(t,n){return J(this,r=>{r._data.nodes.allNodes[t.number].children=r._data.nodes.allNodes[t.number].children.filter(i=>i!==n.number),r._data.nodes.allNodes[n.number].parent=-1})}sortChildren(t,n){return J(this,r=>{r._data.nodes.allNodes[t.number].children=this._data.nodes.allNodes[t.number].children.map(i=>r.getNode(i)).sort(n).map(i=>i.number)})}addChild(t,n){return J(this,r=>{const i=r.getNode(n.number);r.getNode(t.number).children.push(i.number),i.parent=t.number})}setRoot(t){return J(this,n=>{n._data.rootNode=t.number})}}function Os(e,t,n){let r=0;if(e.nodes.allNodes[t.number].children.length>0){const i=new Map;for(const o of e.nodes.allNodes[t.number].children.map(l=>e.nodes.allNodes[l])){const l=Os(e,o,n);i.set(o.number,l),r+=l}const a=e.nodes.allNodes[t.number].children.slice().sort((o,l)=>n(e.nodes.allNodes[o],fe(i.get(o),"Internal error when ordering. Counts not defined."),e.nodes.allNodes[l],fe(i.get(l),"Internal error when ordering. Counts not defined.")));a.reduce((o,l,u)=>o||l!==e.nodes.allNodes[t.number].children[u],!0)&&(e.nodes.allNodes[t.number].children=a)}else r=1;return r}function*zc(e,t=void 0){const n=function*(r){yield e.getNode(r.number);const i=e.getChildCount(r);if(i>0)for(let a=0;a<i;a++){const s=e.getChild(r,a);yield*n(s)}};t===void 0&&(t=e.getRoot()),yield*n(t)}function pt(e,t,n){let r;return e.isRoot(t)?r=Yu(e.getChildren(t).filter(i=>i.number!=n.number),i=>i.number):r=t.number,fe(r,"There was an error finding the path through the root. check the children")}function*Bc(e,t=void 0){const n=function*(r,i=void 0){const a=[...e.getChildren(r)];e.isRoot(r)||a.push(e.getParent(r));const s=a.filter(u=>u.number!==i),o=a.find(u=>u.number===i);s.sort((u,c)=>pt(e,u,r)-pt(e,c,r));let l;!e.isRoot(r)&&o===e.getParent(r)?l=e.getLength(r):o!==void 0&&(l=e.getLength(o));for(const u of s)yield*n(u,r.number);yield{...e.getNode(r.number),pseudoLength:l,pseudoChildren:s,pseudoParent:o}};t===void 0&&(t=e.getRoot()),yield*n(t)}function*js(e,t=void 0){const n=function*(r,i=void 0){const a=[...e.getChildren(r)];e.isRoot(r)||a.push(e.getParent(r));const s=a.filter(u=>u.number!==i),o=a.find(u=>u.number===i);s.sort((u,c)=>pt(e,u,r)-pt(e,c,r));let l;!e.isRoot(r)&&o===e.getParent(r)?l=e.getLength(r):o!==void 0&&(l=e.getLength(o)),yield{...e.getNode(r.number),pseudoLength:l,pseudoChildren:s,pseudoParent:o};for(const u of s)yield*n(u,r.number)};t===void 0&&(t=e.getRoot()),yield*n(t)}function*zs(e,t,n){const r=function*(i,a=void 0){const s=[...e.getChildren(i)];e.isRoot(i)||s.push(e.getParent(i));const o=s.filter(c=>c.number!==a),l=s.find(c=>c.number===a);o.sort((c,h)=>pt(e,c,i)-pt(e,h,i));let u;if(!e.isRoot(i)&&l===e.getParent(i)?u=e.getLength(i):l!==void 0&&(u=e.getLength(l)),o.length==0)yield{...e.getNode(i.number),pseudoLength:u,pseudoChildren:o,pseudoParent:l};else for(const c of o)yield*r(c,i.number)};t===void 0&&(t=e.getRoot()),n!==void 0?yield*r(t,n.number):yield*r(t)}function*Bs(e,t=void 0){const n=function*(r){const i=e.getChildCount(r);if(i>0)for(let a=0;a<i;a++){const s=e.getChild(r,a);yield*n(s)}yield r};t===void 0&&(t=e.getRoot()),yield*n(t)}function*vi(e,t){t===void 0&&(t=e.getRoot());const n=function*(r){const i=e.getChildCount(r);if(i>0)for(let a=0;a<i;a++){const s=e.getChild(r,a);yield*n(s)}else yield r};yield*n(t)}function*Vc(e,t){let n=t;for(;!e.isRoot(n);)yield n,n=e.getParent(n);yield n}function qc(e,t){switch(e.type){case q.BOOLEAN:return[!0,!1];case q.DISCRETE:{const n=e.value;if(t!==void 0){const r=t;return[...new Set([...r,n])].sort()}else return[n]}case q.NUMERICAL:{const n=e.value;return ct([...t||[],n])}case q.DISCRETE_SET:{const n=e.value,r=t||[];return[...new Set([...r,...n])].sort()}case q.NUMERICAL_SET:{const n=e.value;return ct([...t||[],...n])}case q.DENSITIES:if(t!==void 0){const n=t;return[...new Set([...n,...Object.keys(e.value)])].sort()}else return[...new Set(Object.keys(e.value))].sort().filter(n=>n);case q.MARKOV_JUMPS:{const n=e.value.reduce((i,a)=>i.concat([a.to,a.from]),[]),r=t||[];return[...new Set([...r,...n])].sort()}default:throw new Error("Unrecognized type  when updating domain")}}function Hc(){return{lastChunk:"",status:"parsing",end:"",start(){},transform(e,t){const n=this.lastChunk+e;let r="";for(let i=0;i<n.length;i++){const a=n[i];K(a,"Internal Error. Hit empty character in array"),this.status==="parsing"?([this.status,this.end]=Yc(a),this.status==="in comment"&&(r.length>0&&t.enqueue(r),r="")):a===this.end&&(this.status="parsing",this.end=""),this.status==="parsing"&&/\s|;|\]/.test(a)?(r.length>0&&(/\]/.test(a)&&(r+=a),t.enqueue(r),r=""),/;/.test(a)&&t.enqueue(a)):r+=a}this.lastChunk=r},flush(e){this.lastChunk&&e.enqueue(this.lastChunk)}}}function Yc(e){return e==="'"?["in single quote","'"]:e==='"'?["in double quote",'"']:e==="["?["in comment","]"]:["parsing",""]}const pa=/\s*('[^']+'|"[^"]+"|\[&[^[]+]|,|:|\)|\(|;)\s*/;class Wc{reader;taxonSet;currentBlock;hasTree;options;translateTaxonMap;constructor(t,n={}){const r=new TransformStream(Hc());this.reader=t.pipeThrough(new TextDecoderStream).pipeThrough(r).getReader(),this.taxonSet=new an,this.currentBlock=void 0,this.options=n}async*getTrees(){for(;this.currentBlock!=="trees";)await this.parseNextBlock(),this.hasTree=!0;yield*this.parseTreesBlock()}async parseNextBlock(){const t=await this.getNextBlockName();switch(t){case"taxa":this.currentBlock="taxa",await this.parseTaxaBlock();break;case"trees":this.currentBlock="trees";break;default:console.log(`skipping block ${t}. Only parsing blocks are taxa and trees for now.`),await this.readToEndOfBlock()}}async nextToken(){const{done:t,value:n}=await this.reader.read();if(t)throw new Error("unexpectedly hit the end of the stream");return n}async skipSemiColon(){const{done:t,value:n}=await this.reader.read();if(t)throw new Error("unexpectedly hit the end of the stream");if(!n.match(/;$/))throw new Error(`expected ";" got ${n}`)}async getNextBlockName(){let t=!0,n;for(;t;)(await this.nextToken()).match(/\bbegin/i)&&(n=await this.nextToken(),await this.skipSemiColon(),t=!1);return n}async readToEndOfBlock(){let t=!0;for(;t;)(await this.nextToken()).match(/\bend;/i)&&(t=!1)}async skipUntil(t){let n,r=!0;for(;r;)n=await this.nextToken(),t.test(n)&&(r=!1);if(n==null)throw new Error(`Internal parsing error: ${t.source} not found `);return n}async readUntil(t){let n="",r=!0;for(;r;){const i=await this.nextToken();t.test(i)&&(n+=i,r=!1),n+=i}return n}async parseTaxaBlock(){let t,n=!0;for(;n;){const r=await this.skipUntil(/dimensions|taxlabels|end/i);switch(!0){case/dimensions/i.test(r):{const i=await this.readUntil(/;/),a=i.match(/ntax=(\d+);/);if(a)K(a[1],"No number of taxa found despite matching regex"),t=parseInt(a[1]);else throw new Error(`Expected dimension in form of ntax=(\\d+);. Got ${i}`);break}case/taxlabels/i.test(r):{let i=await this.nextToken();for(;i!==";";)this.taxonSet.addTaxon(i),i=await this.nextToken();if(t&&t!=this.taxonSet.getTaxonCount())throw new Error(`found ${this.taxonSet.getTaxonCount()} taxa. Expected: ${t}}`);break}case/end/i.test(r):{if(this.taxonSet.getTaxonCount()===0)throw new Error("hit end of taxa section but didn't find any taxa");this.taxonSet.lockTaxa(),await this.skipSemiColon(),n=!1;break}default:throw new Error(`Reached impossible code looking for dimensions or taxlabels or end in taxa block "${r}"`)}}}async*parseTreesBlock(){let t,n=!0;for(;n;){const r=await this.skipUntil(/translate|tree|end/i);switch(!0){case/translate/i.test(r):{this.translateTaxonMap=new Map;let i=0,a;for(t=await this.nextToken();t!==";";){if(i%2==0)a=t;else{if(t[t.length-1]===","&&(t=t.slice(0,-1)),this.taxonSet.isFinalized){if(!this.taxonSet.hasTaxon(t))throw new Error(`Taxon ${t} not found in taxa block - but found in translate block`)}else this.taxonSet.addTaxon(t);K(a,"Error parsing nexus. Expected key for taxa but found nothing"),this.translateTaxonMap.set(a,t)}for(t=await this.nextToken();t===",";)t=await this.nextToken();i++}this.taxonSet.lockTaxa();break}case/tree/i.test(r):{await this.nextToken();const i=new ks(this.taxonSet,{translateTaxonNames:this.translateTaxonMap});t=await this.skipUntil(/\(/);let a=t.split(pa).filter(o=>o.length>0).reverse();for(;!i.isDone();){for(;a.length>0;){const o=a.pop();K(o,"Unexpectedly hit the end of the buffer"),i.parseCharacter(o)}i.isDone()||(t=await this.nextToken(),a=t.split(pa).filter(o=>o.length>0).reverse())}yield i.getTree();break}case/end/i.test(r):await this.skipSemiColon(),this.hasTree=!1,this.reader.releaseLock(),n=!1;break;default:throw new Error(`Reached impossible code in treeblock block "${r}"`)}}}}class Gc{_forwardCache;_reverseCache;constructor(){this._forwardCache=new Map,this._reverseCache=new Map}*traverse(t,n){const r=function*(i){const a=t.getChildCount(i);if(a>0)for(let s=0;s<a;s++){const o=t.getChild(i,s);yield*r(o)}yield i};n===void 0&&(n=t.getRoot()),yield*r(n)}getNext(t,n){const r=this._forwardCache.get(n);if(r!==void 0&&this._forwardCache.get(r)!==void 0)return r;if(t.isRoot(n))return;const i=t.getParent(n);if(t.hasRightSibling(n)){const a=t.getRightSibling(n);this._forwardCache.set(n,a),this._reverseCache.set(a,n)}else this._forwardCache.set(n,i),this._reverseCache.set(i,n);return this._forwardCache.get(n)}getPrevious(t,n){const r=this._reverseCache.get(n);if(r!==void 0&&this._reverseCache.get(r)!==void 0)return r;if(n!==this.traverse(t).next().value){if(t.isInternal(n)){const i=t.getChildCount(n)-1,a=t.getChild(n,i);this._reverseCache.set(n,a),this._forwardCache.set(a,n)}else if(t.hasLeftSibling(n)){const i=t.getLeftSibling(n);this._reverseCache.set(n,i),this._forwardCache.set(i,n)}else{let i=n;for(;!t.hasLeftSibling(i);)i=t.getParent(i);const a=t.getLeftSibling(i);this._reverseCache.set(n,a),this._forwardCache.set(a,n)}return this._reverseCache.get(n)}}}var 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S.jsx(Gn,{d:x,fill:p,...t,animated:!1},u)})})}function Bf(e){const t=P.useContext(on),n=P.useContext(Ie),{bars:r,attrs:i}=e,a=e.ticks?{...ce.ticks,...e.ticks}:ce.ticks,s=e.title?{...ce.title,...e.title}:ce.title,o=io(e,t);let l;a.values!=null?l=a.values:l=o.ticks(a.number);const u=We(n({x:t.domainX[1],y:t.domainY[1]}).theta),c=t.domainY[1]+t.domainY[1]*.005,h=n({x:t.domainX[0],y:c}),f=n({x:t.domainX[1],y:c}),d=`M${h.x},${h.y} L${f.x},${f.y}`,g=a.length*Math.cos(u),m=a.length*Math.sin(u),x=a.padding*Math.cos(u),p=a.padding*Math.sin(u),b=fe(ci(o.range()),"Error calculating x position for title"),y=n({x:b,y:c}),w=s.padding*Math.cos(u),C=s.padding*Math.sin(u);return S.jsxs("g",{className:"axis",children:[S.jsx(zf,{...r,tickValues:l,scale:o,axisY:c}),":",S.jsx("path",{d,stroke:"black",...i}),S.jsxs("g",{children:[l.map((k,A)=>{const E=n({x:o(k),y:c});return S.jsxs("g",{transform:`translate(${E.x},${E.y}) 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S.jsx(li,{x:c.x,width:f.x-c.x,y:h.y,height:c.y-h.y,fill:d,rx:2,ry:2,...t,animated:!1},`recBar-${u}`)},[])},"axisBars")}function qf(e){const t=P.useContext(on),n=P.useContext(Ie),{gap:r=ce.gap,bars:i}=e,a={...ce.attrs,...e.attrs},s=e.ticks?{...ce.ticks,...e.ticks}:ce.ticks,o=e.title?{...ce.title,...e.title}:ce.title,l=io(e,t);let u;s.values!==void 0?u=s.values:u=l.ticks(s.number);const c=t.domainY[1]+t.domainY[1]*.01,h=n({x:t.domainX[0],y:c}),f=n({x:t.domainX[1],y:c}),d=`M${h.x},${h.y+r} L${f.x},${f.y+r}`,g=fe(ci(l.range()),"Error calculating x position for title"),m=n({x:g,y:c});return S.jsxs("g",{className:"axis",children:[i?S.jsx(Vf,{...i,tickValues:u,scale:l,axisY:c}):null,S.jsx("path",{d,stroke:"black",...a}),S.jsxs("g",{children:[u.map((x,p)=>{const b=n({x:l(x),y:c});return S.jsxs("g",{transform:`translate(${b.x},${b.y+r})`,children:[S.jsx("line",{x1:0,y1:0,x2:0,y2:s.length,stroke:"black",...a}),S.jsx("text",{transform:`translate(0,${s.padding})`,textAnchor:"middle",dominantBaseline:"central",...s.style,children:s.format(x)})]},`tick-${p}`)}),S.jsx("g",{transform:`translate(${m.x},${m.y+r}) `,children:S.jsx("text",{textAnchor:"middle",transform:`translate(0,${o.padding})`,...o.style,children:o.text})})]})]})}function Hf(e){const t=P.useContext(on),{layoutClass:n}=t;return n===Y.Polar?S.jsx(Bf,{...e}):n===Y.Rectangular?S.jsx(qf,{...e}):(console.warn(`Axis not supported for ${n}`),null)}const Yf=bi.fromNewick("((A:1,B:1):1,C:2);"),re={opts:ys,width:100,layout:qs,margins:{top:10,right:10,bottom:10,left:10},tree:Yf,baubles:[ro({filter:()=>!0,attrs:{stroke:"black",strokeWidth:1}})],animated:!1};function Wf(e){const{width:t=re.width,height:n=re.width,margins:r=re.margins,tree:i=re.tree,layout:a=re.layout,animated:s=re.animated,baubles:o=re.baubles,axis:l}=e,u=e.opts?e.opts:re.opts,{rootAngle:c=re.opts.rootAngle,angleRange:h=re.opts.angleRange,fishEye:f=re.opts.fishEye,pollard:d=re.opts.pollard,minRadius:g=re.opts.minRadius,invert:m=re.opts.invert}=u;let x,p,{x:b,y}=e;b!==void 0&&y!==void 0?(x=t,p=n):(x=t-r.left-r.right,p=n-r.top-r.bottom,b=r.left,y=r.top);const w=a(i,u),{layoutClass:C}=w(i.getRoot()),k=ct(i.getNodes().map(N=>w(N).x)).map(N=>fe(N,"Error finding x extent from layout")),A=ct(i.getNodes().map(N=>w(N).y)).map(N=>fe(N,"Error finding y extent from layout")),E={canvasWidth:x,canvasHeight:p,domainX:k,domainY:A,layoutClass:C,invert:m,pollard:d,minRadius:g,fishEye:f,rootAngle:c,angleRange:h},I=Oh(E),j=o.map(N=>If(N,i));return S.jsx("g",{children:S.jsx("g",{transform:`translate(${b},${y})`,children:S.jsx(Ie.Provider,{value:I,children:S.jsx(on.Provider,{value:E,children:S.jsx(vt.Provider,{value:w,children:S.jsxs(wt.Provider,{value:s,children:[l?S.jsx(Hf,{...l}):null,j.map((N,L)=>S.jsx(ff,{...N},N.id??L))]})})})})})})}exports.BaseAnnotationType=q;exports.BranchLabels=Uf;exports.Branches=ro;exports.CartoonClades=jf;exports.CircleNodes=Lf;exports.FigTree=Wf;exports.HighlightClades=Of;exports.ImmutableTree=bi;exports.NexusImporter=Wc;exports.NodeLabels=Df;exports.PreOrderTraversalCache=Gc;exports.RectangleNodes=Ff;exports.TaxonSet=an;exports.dateToDecimal=cc;exports.decimalToDate=lc;exports.defaultInternalLayoutOptions=ys;exports.layoutClass=Y;exports.leapYear=gi;exports.pathToRootIterator=Vc;exports.polarLayout=Qc;exports.postOrderIterator=Bs;exports.preOrderIterator=zc;exports.pseudoTipIterator=zs;exports.psuedoRootPostOrderIterator=Bc;exports.psuedoRootPreOrderIterator=js;exports.radialLayout=Xc;exports.rectangularLayout=qs;exports.tipIterator=vi;